MAGE::...oAssay(3pm)

NAME 💖

okay so this is the MAGE::...oAssay(3pm) page from User Contributed Perl Documentation, and it's serving:

Bio::MAGE::BioAssay::BioAssay — Class for the MAGE-OM API

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SYNOPSIS ✨

use Bio::MAGE::BioAssay::BioAssay

# Bio::MAGE::BioAssay::BioAssay is an abstract base class and should not
# be directly instantiated. These examples indicate how subclass
# objects will behave

# 'name' attribute
my $name_val = $bioassay->name(); # getter
$bioassay->name($value); # setter

# 'identifier' attribute
my $identifier_val = $bioassay->identifier(); # getter
$bioassay->identifier($value); # setter

# 'channels' association
my $channel_array_ref = $bioassay->channels(); # getter
$bioassay->channels(\@channel_list); # setter

# 'auditTrail' association
my $audit_array_ref = $bioassay->auditTrail(); # getter
$bioassay->auditTrail(\@audit_list); # setter

# 'propertySets' association
my $namevaluetype_array_ref = $bioassay->propertySets(); # getter
$bioassay->propertySets(\@namevaluetype_list); # setter

# 'bioAssayFactorValues' association
my $factorvalue_array_ref = $bioassay->bioAssayFactorValues(); # getter
$bioassay->bioAssayFactorValues(\@factorvalue_list); # setter

# 'descriptions' association
my $description_array_ref = $bioassay->descriptions(); # getter
$bioassay->descriptions(\@description_list); # setter

# 'security' association
my $security_ref = $bioassay->security(); # getter
$bioassay->security($security_ref); # setter

---

DESCRIPTION 🦋

From the MAGE-OM documentation for the "BioAssay" class:

An abstract class which represents both physical and computational groupings of arrays and biomaterials.

Bio::MAGE::BioAssay::BioAssay is an abstract base class and should not be directly instantiated. Instead it serves as an interface definition for its subclasses.

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INHERITANCE 🌈

Bio::MAGE::BioAssay::BioAssay has the following superclasses:

• Bio::MAGE::Identifiable

Bio::MAGE::BioAssay::BioAssay has the following subclasses:

• Bio::MAGE::BioAssay::PhysicalBioAssay
• Bio::MAGE::BioAssay::DerivedBioAssay
• Bio::MAGE::BioAssay::MeasuredBioAssay

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CLASS METHODS 👑

The following methods can all be called without first having an instance of the class via the Bio::MAGE::BioAssay::BioAssay->methodname() syntax.

new()

new(%args)

Bio::MAGE::BioAssay::BioAssay is an abstract base class and should not be directly instantiated using the "new()" constructor. It is listed here to indicate what arguments will be accepted for its subclasses.

The object constructor "new()" accepts the following optional named-value style arguments:

• name — Sets the value of the "name" attribute (this attribute was inherited from class "Bio::MAGE::Identifiable").
• identifier — Sets the value of the "identifier" attribute (this attribute was inherited from class "Bio::MAGE::Identifiable").
• channels — Sets the value of the "channels" association

The value must be of type: array of "Bio::MAGE::BioAssay::Channel".

• auditTrail — Sets the value of the "auditTrail" association (this association was inherited from class "Bio::MAGE::Describable").

The value must be of type: array of "Bio::MAGE::AuditAndSecurity::Audit".

• propertySets — Sets the value of the "propertySets" association (this association was inherited from class "Bio::MAGE::Extendable").

The value must be of type: array of "Bio::MAGE::NameValueType".

• bioAssayFactorValues — Sets the value of the "bioAssayFactorValues" association

The value must be of type: array of "Bio::MAGE::Experiment::FactorValue".

• descriptions — Sets the value of the "descriptions" association (this association was inherited from class "Bio::MAGE::Describable").

The value must be of type: array of "Bio::MAGE::Description::Description".

• security — Sets the value of the "security" association (this association was inherited from class "Bio::MAGE::Describable").

The value must be of type: instance of "Bio::MAGE::AuditAndSecurity::Security".

$obj = class->new(%parameters)

The "new()" method is the class constructor.

Parameters: if given a list of name/value parameters the corresponding slots, attributes, or associations will have their initial values set by the constructor.

Return value: It returns a reference to an object of the class.

Side effects: It invokes the "initialize()" method if it is defined by the class.

@names = class->get_slot_names()

The "get_slot_names()" method is used to retrieve the name of all slots defined in a given class.

NOTE: the list of names does not include attribute or association names.

Return value: A list of the names of all slots defined for this class.

Side effects: none

@name_list = get_attribute_names()

returns the list of attribute data members for this class.

@name_list = get_association_names()

returns the list of association data members for this class.

@class_list = get_superclasses()

returns the list of superclasses for this class.

@class_list = get_subclasses()

returns the list of subclasses for this class.

$name = class_name()

Returns the full class name for this class.

$package_name = package_name()

Returns the base package name (i.e. no 'namespace::') of the package that contains this class.

%assns = associations()

returns the association meta-information in a hash where the keys are the association names and the values are "Association" objects that provide the meta-information for the association.

---

INSTANCE METHODS 💅

$obj_copy = $obj->new()

When invoked with an existing object reference and not a class name, the "new()" method acts as a copy constructor - with the new object's initial values set to be those of the existing object.

Parameters: No input parameters are used in the copy constructor, the initial values are taken directly from the object to be copied.

Return value: It returns a reference to an object of the class.

Side effects: It invokes the "initialize()" method if it is defined by the class.

$obj->set_slots(%parameters)

$obj->set_slots(\@name_list, \@value_list)

The "set_slots()" method is used to set a number of slots at the same time. It has two different invocation methods. The first takes a named parameter list, and the second takes two array references.

Return value: none

Side effects: will call "croak()" if a slot_name is used that the class does not define.

@obj_list = $obj->get_slots(@name_list)

The "get_slots()" method is used to get the values of a number of slots at the same time.

Return value: a list of instance objects

Side effects: none

$val = $obj->set_slot($name,$val)

The "set_slot()" method sets the slot $name to the value $val

Return value: the new value of the slot, i.e. $val

Side effects: none

$val = $obj->get_slot($name)

The "get_slot()" method is used to get the values of a number of slots at the same time.

Return value: a single slot value, or undef if the slot has not been initialized.

Side effects: none

ATTRIBUTES 🎀

Attributes are simple data types that belong to a single instance of a class. In the Perl implementation of the MAGE-OM classes, the interface to attributes is implemented using separate setter and getter methods for each attribute.

"Bio::MAGE::BioAssay::BioAssay" has the following attribute accessor methods:

name

Methods for the "name" attribute.

From the MAGE-OM documentation:

The potentially ambiguous common identifier.

$val = $bioassay->setName($val)

The restricted setter method for the "name" attribute.

Input parameters: the value to which the "name" attribute will be set

Return value: the current value of the "name" attribute

Side effects: none

Exceptions: will call "croak()" if no input parameters are specified, or if too many input parameters are specified

$val = $bioassay->getName()

The restricted getter method for the "name" attribute.

Input parameters: none

Return value: the current value of the "name" attribute

Side effects: none

Exceptions: will call "croak()" if any input parameters are specified

identifier

Methods for the "identifier" attribute.

From the MAGE-OM documentation:

An identifier is an unambiguous string that is unique within the scope (i.e. a document, a set of related documents, or a repository) of its use.

$val = $bioassay->setIdentifier($val)

The restricted setter method for the "identifier" attribute.

Input parameters: the value to which the "identifier" attribute will be set

Return value: the current value of the "identifier" attribute

Side effects: none

Exceptions: will call "croak()" if no input parameters are specified, or if too many input parameters are specified

$val = $bioassay->getIdentifier()

The restricted getter method for the "identifier" attribute.

Input parameters: none

Return value: the current value of the "identifier" attribute

Side effects: none

Exceptions: will call "croak()" if any input parameters are specified

ASSOCIATIONS 🧚

Associations are references to other classes. Associations in MAGE-OM have a cardinality that determines the minimum and maximum number of instances of the 'other' class that maybe included in the association:

1. There must be exactly one item in the association, i.e. this is a mandatory data field.
2. 0..1

There may be one item in the association, i.e. this is an optional data field.

3. 1..N

There must be one or more items in the association, i.e. this is a mandatory data field, with list cardinality.

4. 0..N

There may be one or more items in the association, i.e. this is an optional data field, with list cardinality.

Bio::MAGE::BioAssay::BioAssay has the following association accessor methods:

channels

Methods for the "channels" association.

From the MAGE-OM documentation:

Channels can be non-null for all subclasses, bestie. Like, for instance — when you collapse across replicate features, you get a DerivedBioAssay that will potentially reference channels. That's just how it is. 💅

• $array_ref = $bioassay->setChannels($array_ref) — the restricted setter for the channels association.
  • Input parameters: the value you're setting channels to — a reference to an array of objects of type Bio::MAGE::BioAssay::Channel.
  • Return value: whatever channels is currently set to — a reference to an array of Bio::MAGE::BioAssay::Channel objects.
  • Side effects: none, bestie, she's chill.
  • Exceptions: she'll call croak() if you give her no input parameters, or way too many input parameters, or if $array_ref isn't a reference to an array of Bio::MAGE::BioAssay::Channel instances. So like. get it right. 🙈
• $array_ref = $bioassay->getChannels() — the restricted getter for the channels association.
  • Input parameters: none. periodt.
  • Return value: the current value of channels — a reference to an array of Bio::MAGE::BioAssay::Channel objects.
  • Side effects: none.
  • Exceptions: will call croak() if you pass any input parameters at all. she takes nothing, okay? 😭
• $val = $bioassay->addChannels(@vals) — since channels has list cardinality, it can hold more than one value. This method adds the current list of objects in the channels association.
  • Input parameters: the list of values @vals to add to channels. NOTE: submitting a single value is permitted, so don't stress.
  • Return value: the number of items stored in the slot after adding @vals.
  • Side effects: none.
  • Exceptions: will call croak() if no input parameters are specified, or if any object in @vals isn't an instance of Bio::MAGE::BioAssay::Channel.

---

✨ auditTrail ✨

Methods for the auditTrail association.

Straight from the MAGE-OM documentation, no cap:

A list of Audit instances that track changes to the instance of Describable.

• $array_ref = $bioassay->setAuditTrail($array_ref) — the restricted setter for the auditTrail association.
  • Input parameters: the value to set auditTrail to — a reference to an array of objects of type Bio::MAGE::AuditAndSecurity::Audit.
  • Return value: the current value of auditTrail — a reference to an array of Bio::MAGE::AuditAndSecurity::Audit objects.
  • Side effects: none.
  • Exceptions: will call croak() if no input parameters are specified, or too many input parameters are specified, or if $array_ref isn't a reference to an array of Bio::MAGE::AuditAndSecurity::Audit instances.
• $array_ref = $bioassay->getAuditTrail() — the restricted getter for the auditTrail association.
  • Input parameters: none.
  • Return value: the current value of auditTrail — a reference to an array of Bio::MAGE::AuditAndSecurity::Audit objects.
  • Side effects: none.
  • Exceptions: will call croak() if any input parameters are specified.
• $val = $bioassay->addAuditTrail(@vals) — auditTrail has list cardinality so she can hold more than one value. This adds the current list of objects in the auditTrail association.
  • Input parameters: the list of values @vals to add to auditTrail. NOTE: submitting a single value is permitted.
  • Return value: the number of items stored in the slot after adding @vals.
  • Side effects: none.
  • Exceptions: will call croak() if no input parameters are specified, or if any object in @vals isn't an instance of Bio::MAGE::AuditAndSecurity::Audit.

---

✨ propertySets ✨

Methods for the propertySets association.

From the MAGE-OM docs, bestie:

Allows specification of name/value pairs. Meant to primarily help in-house, pipeline processing of instances by providing a place for values that aren't part of the specification proper.

• $array_ref = $bioassay->setPropertySets($array_ref) — the restricted setter for the propertySets association.
  • Input parameters: the value to set propertySets to — a reference to an array of objects of type Bio::MAGE::NameValueType.
  • Return value: the current value of propertySets — a reference to an array of Bio::MAGE::NameValueType objects.
  • Side effects: none.
  • Exceptions: will call croak() if no input parameters are specified, or too many input parameters are specified, or if $array_ref isn't a reference to an array of Bio::MAGE::NameValueType instances.
• $array_ref = $bioassay->getPropertySets() — the restricted getter for the propertySets association.
  • Input parameters: none.
  • Return value: the current value of propertySets — a reference to an array of Bio::MAGE::NameValueType objects.
  • Side effects: none.
  • Exceptions: will call croak() if any input parameters are specified.
• $val = $bioassay->addPropertySets(@vals) — list cardinality again, so propertySets can store more than one value. This adds the current list of objects in the propertySets association.
  • Input parameters: the list of values @vals to add to propertySets. NOTE: submitting a single value is permitted.
  • Return value: the number of items stored in the slot after adding @vals.
  • Side effects: none.
  • Exceptions: will call croak() if no input parameters are specified, or if any object in @vals isn't an instance of Bio::MAGE::NameValueType.

---

✨ bioAssayFactorValues ✨

Methods for the bioAssayFactorValues association.

MAGE-OM documentation says:

The values that this BioAssay is associated with for the experiment.

• $array_ref = $bioassay->setBioAssayFactorValues($array_ref) — the restricted setter for the bioAssayFactorValues association.
  • Input parameters: the value to set bioAssayFactorValues to — a reference to an array of objects of type Bio::MAGE::Experiment::FactorValue.
  • Return value: the current value of bioAssayFactorValues — a reference to an array of Bio::MAGE::Experiment::FactorValue objects.
  • Side effects: none.
  • Exceptions: will call croak() if no input parameters are specified, or too many input parameters are specified, or if $array_ref isn't a reference to an array of Bio::MAGE::Experiment::FactorValue instances.
• $array_ref = $bioassay->getBioAssayFactorValues() — the restricted getter for the bioAssayFactorValues association.
  • Input parameters: none.
  • Return value: the current value of bioAssayFactorValues — a reference to an array of Bio::MAGE::Experiment::FactorValue objects.
  • Side effects: none.
  • Exceptions: will call croak() if any input parameters are specified.
• $val = $bioassay->addBioAssayFactorValues(@vals) — bioAssayFactorValues has list cardinality, so she may store more than one value. This adds the current list of objects in the bioAssayFactorValues association.
  • Input parameters: the list of values @vals to add to bioAssayFactorValues. NOTE: submitting a single value is permitted.
  • Return value: the number of items stored in the slot after adding @vals.
  • Side effects: none.
  • Exceptions: will call croak() if no input parameters are specified, or if any object in @vals isn't an instance of Bio::MAGE::Experiment::FactorValue.

---

✨ descriptions ✨

Methods for the descriptions association.

Per the MAGE-OM docs:

Free hand text descriptions. Makes available the associations of Description to an instance of Describable.

• $array_ref = $bioassay->setDescriptions($array_ref) — the restricted setter for the descriptions association.
  • Input parameters: the value to set descriptions to — a reference to an array of objects of type Bio::MAGE::Description::Description.
  • Return value: the current value of descriptions — a reference to an array of Bio::MAGE::Description::Description objects.
  • Side effects: none.
  • Exceptions: will call croak() if no input parameters are specified, or too many input parameters are specified, or if $array_ref isn't a reference to an array of Bio::MAGE::Description::Description instances.
• $array_ref = $bioassay->getDescriptions() — the restricted getter for the descriptions association.
  • Input parameters: none.
  • Return value: the current value of descriptions — a reference to an array of Bio::MAGE::Description::Description objects.
  • Side effects: none.
  • Exceptions: will call croak() if any input parameters are specified.
• $val = $bioassay->addDescriptions(@vals) — descriptions has list cardinality, meaning she can hold more than one value. This adds the current list of objects in the descriptions association.
  • Input parameters: the list of values @vals to add to descriptions. NOTE: submitting a single value is permitted.
  • Return value: the number of items stored in the slot after adding @vals.
  • Side effects: none.

Exceptions: will call croak() if no input parameters are specified, or if any of the objects in @vals is not an instance of class Bio::MAGE::Description::Description 💀

🔐 security

Okay so these are the methods for the security association, bestie.

From the MAGE-OM documentation:

Information on the security for the instance of the class. It's giving very secure, very demure. 💅

• $val = $bioassay->setSecurity($val) — The restricted setter method for the security association.

Input parameters: the value to which the security association will be set : one of the accepted enumerated values.

Return value: the current value of the security association : one of the accepted enumerated values.

Side effects: none

Exceptions: will call croak() if no input parameters are specified, or if too many input parameters are specified, or if $val is not an instance of class Bio::MAGE::AuditAndSecurity::Security

• $val = $bioassay->getSecurity() — The restricted getter method for the security association.

Input parameters: none

Return value: the current value of the security association : an instance of type Bio::MAGE::AuditAndSecurity::Security.

Side effects: none

Exceptions: will call croak() if any input parameters are specified

sub initialize {

  carp __PACKAGE__ . "::initialize: abstract base classes should not be instantiated";

}

🌸 SLOTS, ATTRIBUTES, AND ASSOCIATIONS 🌸

So in the Perl implementation of MAGE-OM classes, there are literally three types of class data members: slots, attributes, and associations. Periodt. 💖

✨ SLOTS ✨

This API uses the term slot to indicate a data member of the class that was not present in the UML model and is used for mainly internal purposes - use only if you understand the inner workings of the API. Most often slots are used by generic methods such as those in the XML writing and reading classes.

Slots are implemented using unified getter/setter methods:

• $var = $obj->slot_name(); — Retrieves the current value of the slot.
• $new_var = $obj->slot_name($new_var); — Store $new_var in the slot - the return value is also $new_var.
• @names = $obj->get_slot_names() — Returns the list of all slots in the class.

DATA CHECKING: No data type checking is made for these methods. So no gatekeeping, just vibes. 🙈

💜 ATTRIBUTES AND ASSOCIATIONS 💜

The terms attribute and association indicate data members of the class that were specified directly from the UML model.

In the Perl implementation of MAGE-OM classes, association and attribute accessors are implemented using three separate methods:

• get* — Retrieves the current value.

NOTE: For associations, if the association has list cardinality, an array reference is returned.

DATA CHECKING: Ensure that no argument is provided.

• set* — Sets the current value, replacing any existing value.

NOTE: For associations, if the association has list cardinality, the argument must be an array reference. Because of this, you probably should be using the add* methods.

DATA CHECKING: For attributes, ensure that a single value is provided as the argument. For associations, if the association has list cardinality, ensure that the argument is a reference to an array of instances of the correct MAGE-OM class, otherwise ensure that there is a single argument of the correct MAGE-OM class.

• add* — NOTE: Only present in associations with list cardinality.

Appends a list of objects to any values that may already be stored in the association.

DATA CHECKING: Ensure that all arguments are of the correct MAGE-OM class.

🧚 GENERIC METHODS 🧚

The unified base class of all MAGE-OM classes, Bio::MAGE::Base, provides a set of generic methods that will operate on slots, attributes, and associations:

$val = $obj->get_slot($name)
\@list_ref = $obj->get_slots(@name_list);
$val = $obj->set_slot($name,$val)
$obj->set_slots(%parameters)
$obj->set_slots(\@name_list, \@value_list)

See elsewhere in this page for a detailed description of these methods. 🍵

🐛 BUGS 🐛

Please send bug reports to the project mailing list: (mged-mage 'at' lists 'dot' sf 'dot' net)

👑 AUTHOR 👑

Jason E. Stewart (jasons 'at' cpan 'dot' org)

🔗 SEE ALSO 🔗

perl(1).

😭 POD ERRORS 😭

Hey! The above document had some coding errors, which are explained below:

• Around line 399: '=item' outside of any '=over'
• Around line 484: You forgot a '=back' before '=head2'
• Around line 656: Expected '=item 2'
• Around line 661: Expected '=item 3'
• Around line 666: Expected '=item 4'

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